SMTL ID : 8fww.1

Structure of the ligand-binding and transmembrane domains of kainate receptor GluK2 in complex with the positive allosteric modulator BPAM344 and noncompetitive inhibitor perampanel

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: R.543, N.546, L.729, T.730 Ligands: NAG.11 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain B: R.748, N.749, C.750, N.751 Ligands: NAG-NAG-BMA-BMA.2 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.748, B:C.750 NAG-NAG.4: 5 residues within 4Å: Chain C: R.543, N.546, L.729, T.730 Ligands: NAG.30 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain D: R.748, N.749, C.750, N.751 Ligands: NAG-NAG-BMA-BMA.5 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.748, D:C.750

2 x NAG- NAG- BMA- BMA: beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA.2: 6 residues within 4Å: Chain B: R.543, N.546, T.548, T.730, N.751 Ligands: NAG-NAG.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.543 NAG-NAG-BMA-BMA.5: 5 residues within 4Å: Chain D: R.543, N.546, T.548, T.730 Ligands: NAG-NAG.6 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.543

4 x 2J9: 4-cyclopropyl-7-fluoro-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide(Non-covalent)

2J9.7: 15 residues within 4Å: Chain A: K.531, P.532, F.533, M.534, T.535, L.783, Q.786, L.791 Chain D: I.519, P.532, M.534, T.535, S.761, K.762, G.763 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:P.532, A:T.535, A:L.791 Halogen bonds: D:M.534 2J9.15: 14 residues within 4Å: Chain A: I.519, P.532, M.534, T.535, S.761, K.762, G.763 Chain D: K.531, P.532, F.533, M.534, T.535, L.783, Q.786 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:P.532, D:T.535 Halogen bonds: A:M.534 2J9.21: 14 residues within 4Å: Chain B: K.531, P.532, F.533, M.534, T.535, L.783, Q.786 Chain C: I.519, P.532, M.534, T.535, S.761, K.762, G.763 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:P.532, B:T.535 Halogen bonds: C:M.534 2J9.24: 14 residues within 4Å: Chain B: I.519, P.532, M.534, T.535, S.761, K.762, G.763 Chain C: K.531, P.532, F.533, M.534, T.535, L.783, Q.786 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:P.532, C:T.535 Halogen bonds: B:M.534

16 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.8: 18 residues within 4Å: Chain A: V.552, F.553, L.556, N.557, P.561, W.564, M.565, L.568, V.616, L.619, M.620, I.647, Y.651, V.826 Chain D: I.639, F.642, L.645 Ligands: POV.9 Ligand excluded by PLIP POV.9: 13 residues within 4Å: Chain A: V.552, F.553, L.568, L.572, W.613, V.616, A.829, L.833 Chain D: L.631, R.634, I.635 Ligands: POV.8, POV.35 Ligand excluded by PLIP POV.10: 7 residues within 4Å: Chain A: V.817, Q.818, I.825, L.831, V.832 Chain D: Y.566, G.573 Ligand excluded by PLIP POV.13: 15 residues within 4Å: Chain A: L.631, R.634, I.635, I.639 Chain B: L.609, F.612, W.613, I.825, V.826, A.829, G.830, L.833 Ligands: POV.14, POV.22, POV.23 Ligand excluded by PLIP POV.14: 8 residues within 4Å: Chain A: Y.587 Chain B: L.572, L.609, F.612, L.833, F.836 Ligands: POV.13, POV.22 Ligand excluded by PLIP POV.22: 19 residues within 4Å: Chain A: G.638, I.639, F.642, L.645 Chain B: P.550, G.551, F.553, S.554, L.556, W.564, V.567, L.568, V.616, L.619, M.620, I.648, V.826 Ligands: POV.13, POV.14 Ligand excluded by PLIP POV.23: 13 residues within 4Å: Chain A: Y.566, G.573, C.576 Chain B: N.549, V.552, V.817, Q.818, F.824, I.825, A.828, L.831, V.832 Ligands: POV.13 Ligand excluded by PLIP POV.25: 11 residues within 4Å: Chain B: Y.587, I.635 Chain C: L.608, L.609, F.612, L.833, F.836, G.840, E.841, Y.844 Ligands: POV.28 Ligand excluded by PLIP POV.27: 19 residues within 4Å: Chain B: I.639, F.642, L.645 Chain C: V.552, F.553, L.556, N.557, P.561, W.564, M.565, L.568, V.616, L.619, M.620, I.647, I.648, Y.651, V.826 Ligands: POV.28 Ligand excluded by PLIP POV.28: 17 residues within 4Å: Chain B: L.631, R.634, I.635, G.638 Chain C: V.552, F.553, L.568, L.572, L.609, F.612, W.613, V.616, I.825, A.829, L.833 Ligands: POV.25, POV.27 Ligand excluded by PLIP POV.29: 10 residues within 4Å: Chain B: Y.566, G.573 Chain C: V.817, Q.818, G.821, I.825, A.828, A.829, L.831, V.832 Ligand excluded by PLIP POV.32: 7 residues within 4Å: Chain C: Y.587 Chain D: L.572, L.609, F.612, L.833, F.836 Ligands: POV.37 Ligand excluded by PLIP POV.35: 11 residues within 4Å: Chain A: L.608, L.609, F.612, L.833, F.836, G.840, E.841, Y.844 Chain D: Y.587, I.635 Ligands: POV.9 Ligand excluded by PLIP POV.36: 20 residues within 4Å: Chain C: G.638, I.639, F.642, L.645 Chain D: P.550, G.551, F.553, S.554, L.556, W.564, V.567, L.568, C.571, V.616, L.619, M.620, I.647, I.648, V.826 Ligands: POV.37 Ligand excluded by PLIP POV.37: 15 residues within 4Å: Chain C: R.634, I.635 Chain D: F.553, L.568, L.609, F.612, W.613, I.825, V.826, A.829, G.830, L.833 Ligands: POV.32, POV.36, POV.38 Ligand excluded by PLIP POV.38: 14 residues within 4Å: Chain C: G.573, V.574, C.576, V.577 Chain D: N.549, V.552, V.817, Q.818, F.824, I.825, A.828, L.831, V.832 Ligands: POV.37 Ligand excluded by PLIP

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.11: 4 residues within 4Å: Chain A: R.543, N.749, N.751 Ligands: NAG-NAG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.543, A:N.751 NAG.30: 4 residues within 4Å: Chain C: R.543, N.749, N.751 Ligands: NAG-NAG.4 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.543, C:N.751

2 x 6ZP: 2-(6'-oxo-1'-phenyl[1',6'-dihydro[2,3'-bipyridine]]-5'-yl)benzonitrile(Non-covalent)

6ZP.12: 16 residues within 4Å: Chain A: N.549, P.550, S.554, F.555, N.557, P.558, Y.651, N.654, L.655, F.658, L.815, N.819 Chain B: A.812, S.813, A.814 Chain D: S.650 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.550, A:F.555, A:N.557, A:L.655, A:L.655, A:F.658 Hydrogen bonds: A:N.819 6ZP.31: 15 residues within 4Å: Chain B: S.650 Chain C: N.549, P.550, S.554, F.555, N.557, P.558, Y.651, N.654, L.655, F.658, L.659, L.815, N.819 Chain D: A.812 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:P.550, C:F.555, C:N.557, C:P.558, C:L.655, C:L.655, C:F.658, C:F.658, C:F.658, C:F.658 Hydrogen bonds: C:N.819

7 x NA: SODIUM ION(Non-functional Binders)

NA.16: 4 residues within 4Å: Chain A: Q.621 Chain B: Q.621 Chain C: Q.621 Chain D: Q.621 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.621 NA.17: 2 residues within 4Å: Chain A: T.652, A.656 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.652 NA.18: 7 residues within 4Å: Chain A: A.656, T.660 Chain B: A.656, T.660 Chain C: A.656, T.660 Chain D: T.660 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D, 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:T.660, D:T.660, D:T.660, C:T.660, A:T.660 NA.19: 4 residues within 4Å: Chain A: D.528, M.770, R.775 Chain D: D.776 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:R.775, D:D.776 NA.26: 4 residues within 4Å: Chain B: E.524, I.527, D.528 Chain C: I.780 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.524 NA.33: 4 residues within 4Å: Chain B: D.776 Chain C: D.528, M.770, R.775 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.528, C:R.775 NA.39: 4 residues within 4Å: Chain A: I.780 Chain D: E.524, I.527, D.528 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.528

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.20: 3 residues within 4Å: Chain A: K.531, R.775 Chain D: K.531 Ligand excluded by PLIP CL.34: 3 residues within 4Å: Chain B: K.531 Chain C: K.531, R.775 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gangwar, S.P. et al., Positive and negative allosteric modulation of GluK2 kainate receptors by BPAM344 and antiepileptic perampanel. Cell Rep (2023)

Release Date

2023-04-19

Peptides

Glutamate receptor ionotropic, kainate 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Glutamate receptor ionotropic, kainate 2

Related Entries With Identical Sequence